From: Yarrow Madrona (amadrona_at_uci.edu)
Date: Fri May 10 2013 - 14:11:00 CDT
No,
I think one of the input files was corrupted. Anyway, reran previous two
jobs with new input files and everything runs o.k. Computers......sheesh.
-Yarrow
> are you out of disk space/quota?
>
>
> On Thu, May 9, 2013 at 8:25 PM, Yarrow Madrona <amadrona_at_uci.edu> wrote:
>
>> Hello NAMD Gurus,
>>
>> I have created 5 DCD's in succession by restarting from the previous
>> restart files. Any help would be appreciated. I can't figure out why it
>> can't write the restart files for the sixth run.
>> However, on the sixth run i get the following error message:
>>
>> FINISHED WRITING RESTART COORDINATES
>> WRITING VELOCITIES TO RESTART FILE AT STEP 2993000
>> FINISHED WRITING RESTART VELOCITIES
>> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 2993000
>> WRITING COORDINATES TO DCD FILE AT STEP 2994000
>> WRITING COORDINATES TO RESTART FILE AT STEP 2994000
>> FATAL ERROR: Error on write to binary file eq006.restart.coor:
>> Input/output error
>> [0] Stack Traceback:
>> [0:0] _Z8NAMD_errPKc+0xba [0x53de7a]
>> [0:1] _ZN6Output10coordinateEiiP6VectorP11FloatVectorR7Lattice+0xb5d
>> [0xa00a5d]
>> [0:2]
>>
>> _ZN24CkIndex_CollectionMaster39_call_receivePositions_CollectVectorMsgEPvP16CollectionMaster+0xcde
>> [0x54fb1e]
>> [0:3] _Z15_processHandlerPvP11CkCoreState+0x810 [0xb36e90]
>> [0:4] CsdScheduler+0x411 [0xc37a21]
>> [0:5] _ZN9ScriptTcl7Tcl_runEPvP10Tcl_InterpiPPc+0x25d [0xa77fdd]
>> [0:6] TclInvokeStringCommand+0x88 [0xc8a128]
>> [0:7] [0xc8cd47]
>> [0:8] [0xc8e162]
>> [0:9] Tcl_EvalEx+0x16 [0xc8e986]
>> [0:10] Tcl_FSEvalFileEx+0x151 [0xcf0b31]
>> [0:11] Tcl_EvalFile+0x2e [0xcf0cee]
>> [0:12] _ZN9ScriptTcl4loadEPc+0xf [0xa7655f]
>> [0:13] main+0x425 [0x541e85]
>> [0:14] __libc_start_main+0xfd [0x35f4e1ecdd]
>> [0:15] [0x4fafe9]
>> TACC: MPI job exited with code: 1
>>
>> TACC: Shutdown complete. Exiting.
>>
>>
>> 28794,1
>>
>>
>>
>>
>>
>>
>> Bot
>>
>>
>>
>>
>>
>> --
>> Yarrow Madrona
>>
>> Graduate Student
>> Molecular Biology and Biochemistry Dept.
>> University of California, Irvine
>> Natural Sciences I, Rm 2403
>> Irvine, CA 92697
>>
>>
>>
>>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
>
-- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697
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